Cytoscape is an open source
bioinformatics platform for visualizing molecular interaction networks
and integrating these with expression profiles and other high throughput
data sets. This collection of R Markdown Notebooks includes training
vignettes, detailed workflows and community contributed examples of
Cytoscape automation.
These notebooks rely on the RCy3
package available from Bioconductor.
Please cite: RCy3: Networkbiology
using Cytoscape from within R
How to Use
Browse the Table of Contents menu above to find
notebooks rendered as interactive HTML. Notebooks include an option to
download the source Rmd file via the option button labeled ‘code’ at the
top-right of each page.
The Wiki menu option will take you to the overview
documentation for all scripting and app-related automation resources
for Cytoscape.
The Repo menu option will take you to the R
folder of the cytoscape automation GitHub repository.
The Home menu option will bring you back here.
How to Contribute
If you have an R script or notebook involving Cytoscape, please
considering contributing to this central collection. You can either:
- Open a New
Issue pointing to your content and tag it with the label, “new
script or notebook”. Or,
- Fork the
automation repo, push your content to the appropriate folder, and
make a Pull Request. For example, Rmd files that you want to have built
as notebooks and included in this site should go in the
for-scripters/R/notebooks/ folder. See developer
notes for how we build and maintain this notebook collection site.
Return to: Automation
Home
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